diff srf2fastq/io_lib-1.12.2/io_lib/scf.h @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/scf.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,447 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+/*
+ * File: scf.h
+ * Version: 3.00
+ *
+ * Description: file structure definitions for SCF file
+ *
+ * Created: 19 November 1992
+ *
+ */
+
+#ifndef _SCF_H_
+#define _SCF_H_
+
+#include <stdio.h>
+#include <sys/types.h>
+
+#include "io_lib/mFILE.h"
+#include "io_lib/os.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ *-----------------------------------------------------------------------------
+ * Macros
+ *-----------------------------------------------------------------------------
+ */
+
+/* The SCF magic number */
+#define SCF_MAGIC (((((uint_4)'.'<<8)+(uint_4)'s'<<8)+(uint_4)'c'<<8)+(uint_4)'f')
+
+/* prior to this was a different format */
+#define SCF_VERSION_OLDEST 2.00
+#define SCF_VERSION_OLD 2.02
+
+/* The current SCF format level */
+#define SCF_VERSION 3.00
+
+/* Uncertainty code sets supported */
+#define CSET_DEFAULT 0  /* {A,C,G,T,-} */
+#define CSET_STADEN  1 
+#define CSET_NC_IUB  2  /* Pharmacia A.L.F. */
+#define CSET_ALF     3  /* extended NC_IUB */
+#define CSET_ABI     4  /* {A,C,G,T,N} */
+#define CSET_IBI     5  /* IBI/Pustell */
+#define CSET_DNASTAR 6  /* DNA* */
+#define CSET_DNASIS  7
+#define CSET_PCGENE  8  /* IG/PC-Gene */
+#define CSET_GENIE   9  /* MicroGenie */
+
+/* define samples to delta_delta values */
+#define DELTA_IT 1
+
+/* What components to read */
+#define READ_BASES	(1<<0)
+#define READ_SAMPLES	(1<<1)
+#define READ_COMMENTS	(1<<2)
+#define READ_ALL	(READ_BASES | READ_SAMPLES | READ_COMMENTS)
+
+/*
+ *-----------------------------------------------------------------------------
+ * Structures and typedefs
+ *-----------------------------------------------------------------------------
+ */
+
+/*
+ * Type definition for the Header structure
+ */
+typedef struct {
+    uint_4 magic_number;       /* SCF_MAGIC */
+    uint_4 samples;            /* Number of elements in Samples matrix */
+    uint_4 samples_offset;     /* Byte offset from start of file */
+    uint_4 bases;              /* Number of bases in Bases matrix */
+    uint_4 bases_left_clip;    /* OBSOLETE: No. bases in left clip (vector) */
+    uint_4 bases_right_clip;   /* OBSOLETE: No. bases in right clip (qual) */
+    uint_4 bases_offset;       /* Byte offset from start of file */
+    uint_4 comments_size;      /* Number of bytes in Comment section */
+    uint_4 comments_offset;    /* Byte offset from start of file */
+    char   version[4];	       /* "version.revision" */
+    uint_4 sample_size;	       /* precision of samples (in bytes) */
+    uint_4 code_set;	       /* uncertainty codes used */
+    uint_4 private_size;       /* size of private data, 0 if none */
+    uint_4 private_offset;     /* Byte offset from start of file */
+    uint_4 spare[18];          /* Unused */
+} Header;
+
+/*
+ * Header.sample_size == 1.
+ */
+typedef struct {
+    uint_1 sample_A;			/* Sample for A trace */
+    uint_1 sample_C;			/* Sample for C trace */
+    uint_1 sample_G;			/* Sample for G trace */
+    uint_1 sample_T;			/* Sample for T trace */
+} Samples1;
+
+/*
+ * Header.sample_size == 2.
+ */
+typedef struct {
+    uint_2 sample_A;			/* Sample for A trace */
+    uint_2 sample_C;			/* Sample for C trace */
+    uint_2 sample_G;			/* Sample for G trace */
+    uint_2 sample_T;			/* Sample for T trace */
+} Samples2;
+
+/*
+ * Type definition for the sequence data
+ */
+typedef struct {
+    uint_4 peak_index;        /* Index into Samples matrix for base position */
+    uint_1 prob_A;            /* Probability of it being an A */
+    uint_1 prob_C;            /* Probability of it being an C */
+    uint_1 prob_G;            /* Probability of it being an G */
+    uint_1 prob_T;            /* Probability of it being an T */
+    char base;		      /* Base called */
+    uint_1 spare[3];          /* Spare */
+} Bases;
+
+
+/*
+ * Type definition for the comments
+ */
+typedef char Comments;      /* Zero terminated list of \n separated entries */
+
+
+/*
+ * All of the above structs in a single scf format.
+ */
+typedef struct {
+    Header header;
+    union Samples {
+	Samples1 *samples1;
+	Samples2 *samples2;
+    } samples;
+    Bases *bases;
+    Comments *comments;
+    char *private_data;
+} Scf;
+
+/*
+ *-----------------------------------------------------------------------------
+ * Function prototypes
+ *-----------------------------------------------------------------------------
+ */
+
+/*
+ * Reading SCF Files
+ * -----------------
+ */
+
+/*
+ * Read the Header struct.
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_header(mFILE *fp, Header *h);
+
+/*
+ * Read a single 8bit sample
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_sample1(mFILE *fp, Samples1 *s);
+
+/*
+ * Read several 8bit samples
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_samples1(mFILE *fp, Samples1 *s, size_t num_samples);
+
+/*
+ * Read several 8bit samples in delta_delta format
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_samples31(mFILE *fp, Samples1 *s, size_t num_samples);
+
+/*
+ * Read a single 16bit sample
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_sample2(mFILE *fp, Samples2 *s);
+
+/*
+ * Read several 16bit samples
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_samples2(mFILE *fp, Samples2 *s, size_t num_samples);
+
+/*
+ * Read several 16bit samples in delta_delta format
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_samples32(mFILE *fp, Samples2 *s, size_t num_samples);
+
+/*
+ * Read a single Bases structure
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_base(mFILE *fp, Bases *b);
+
+/*
+ * Read several Bases structures consecutively
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_bases(mFILE *fp, Bases *b, size_t num_bases);
+
+/*
+ * Read Bases, peak_indexes and probs
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_bases3(mFILE *fp, Bases *b, size_t num_bases);
+
+/*
+ * Read the SCF Comments.
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int read_scf_comment(mFILE *fp, Comments *c, size_t l);
+
+/*
+ * Reads a whole SCF file into a Scf structure. This memory for this
+ * structure is allocated by this routine. To free this memory use
+ * scf_deallocate().
+ * Returns:
+ *    Scf *	- Success, the Scf structure read.
+ *    NULL	- Failure.
+ * On failure NULL is returned, otherwise the Scf struct.
+ */
+Scf *read_scf(char *fn);
+Scf *fread_scf(FILE *fp);
+Scf *mfread_scf(mFILE *fp);
+
+
+/*
+ * Writing SCF Files
+ * -----------------
+ */
+
+/*
+ * Write the Header struct.
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_header(mFILE *fp, Header *h);
+
+/*
+ * Write a single 8bit sample
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_sample1(mFILE *fp, Samples1 *s);
+
+/*
+ * Write several 8bit samples
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_samples1(mFILE *fp, Samples1 *s, size_t num_samples);
+
+/*
+ * Write several 8bit samples in delta_delta format
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_samples31(mFILE *fp, Samples1 *s, size_t num_samples);
+
+/*
+ * Write 16bit samples
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_sample2(mFILE *fp, Samples2 *s);
+
+/*
+ * Write several 16bit samples
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_samples2(mFILE *fp, Samples2 *s, size_t num_samples);
+
+/*
+ * Write several 16bit samples in delta_delta format
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_samples32(mFILE *fp, Samples2 *s, size_t num_samples);
+
+/*
+ * Write the Bases structure
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_base(mFILE *fp, Bases *b);
+
+/*
+ * Write the several Bases structures consecutively
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_bases(mFILE *fp, Bases *b, size_t num_bases);
+
+/*
+ * Write the bases, then peak indexes, then probs
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_bases3(mFILE *fp, Bases *b, size_t num_bases);
+
+/*
+ * Write the SCF Comments.
+ * Returns:
+ *    0 - success
+ *   -1 - failure
+ */
+int write_scf_comment(mFILE *fp, Comments *c, size_t l);
+
+
+/*
+ * Writes a whole Scf structure to filename "fn".
+ * This initialises several fields in the Header struct for you. These are:
+ *     samples_offset
+ *     bases_offset
+ *     comments_offset
+ *     magic_number
+ *
+ * All other fields are assumed to be correctly set.
+ *
+ * Returns:
+ *     0 for success
+ *    -1 for failure
+ */
+int write_scf(Scf *scf, char *fn);
+int fwrite_scf(Scf *scf, FILE *fp);
+int mfwrite_scf(Scf *scf, mFILE *fp);
+
+/*
+ * Request which (major) version of scf to use when writing.
+ * Defaults to the latest. Currently suitable fields are
+ * 2 and 3.
+ *
+ * Returns 0 for success, -1 for failure.
+ */
+int set_scf_version(int version);
+
+
+/*
+ * Miscellaneous SCF utilities
+ * ---------------------------
+ */
+
+/*
+ * Converts an SCF version string (eg "2.00") to a float
+ */
+float scf_version_str2float(char version[]);
+
+/*
+ * Converts an SCF version float (eg 2.00) to a string
+ * Returns:
+ *    A statically allocated 5 character string.
+ */
+char *scf_version_float2str(float f);
+
+/*
+ * Allocates memory for the scf elements based upon arguments passed.
+ * Returns;
+ *    Scf *	- Success. The scf structure and it's samples, bases,
+ *                and comments fields have been allocated.
+ *    NULL	- Failure.
+ */
+Scf *scf_allocate(int num_samples, int sample_size, int num_bases,
+		  int comment_size, int private_size);
+
+/*
+ * Frees memory allocated by scf_allocate.
+ */
+void scf_deallocate(Scf *scf);
+
+/*
+ * Checks to see if the file with name "fn" is in SCF format.
+ * Returns:
+ *   1  - is in SCF format
+ *   0  - is not in SCF format
+ *  -1  - failure
+ */
+int is_scf(char *fn);
+
+/*
+ * Change sample points to delta_delta values for uint1
+ */
+void scf_delta_samples1 ( int1 samples[], int num_samples, int job);
+
+/*
+ * Change sample points to delta_delta values for uint2
+ */
+void scf_delta_samples2 ( uint2 samples[], int num_samples, int job);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*_SCF_H_*/
+